## [1] "data/config.vertebrata_minimal.yaml"

Analysis report - 22 January, 2023 - 19:51 CET - version: 0.9.7

Setup

Location of genomes files:

results/assemblies

Total number of included genomes: 0
Locally provided genomes: 0
Successfully downloaded genomes: 0
Failed species downloads: 0
Not downloaded:

Information on successfully downloaded genomes:

info <- ""
if (file.exists(downloaded_genomes_statistics_file))
{
  if (file.size(downloaded_genomes_statistics_file) != 0) {
      data <- read.csv(downloaded_genomes_statistics_file, sep="\t", header=T)
  } else {
    info <- "*No information about downloaded genomes found. Maybe you only have local species?*"
  }
  
  data %>% kbl(escape=F) %>% kable_paper("hover", full_width = F) %>% scroll_box(width = "100%", height = "600px") # %>% mutate(ftp_path = cell_spec("download", "html", link = ftp_path)) %>% kbl(escape=F) %>% kable_paper("hover", full_width = F) %>% scroll_box(width = "100%", height = "600px")
} else {
  info <- "*No information about downloaded genomes found. Did you run phylociraptor setup ?*"
}

No information about downloaded genomes found. Did you run phylociraptor setup ?

Orthology

Orthologous genes were inferred using BUSCO.

Location of BUSCO results:

results/orthology/busco

Used BUSCO set: vertebrata_odb10

Total number of BUSCO genes in BUSCO set: 20
Number of BUSCO genes recovered in too few (20) samples: 3
BUSCO genes below threshold:
228730at7742, 164538at7742, 320238at7742

Number of samples with single-copy BUSCO score below threshold (0.5): 0
Genomes below threshold:

species single_copy duplicated fragmented missing
Amblyraja_radiata 2999 71 98 186
Anolis_carolinensis 2861 22 169 302
Callorhinchus_milii 2976 34 131 213
Canis_lupus 3122 47 65 120
Danio_kyathit 3107 45 75 127
Dasypus_novemcinctus 2717 61 212 364
Eptatretus_burgeri 1612 59 490 1193
Gallus_gallus 3180 29 45 100
Homo_sapiens 2984 130 77 163
Latimeria_chalumnae 2795 30 279 250
Loxodonta_africana 3039 22 103 190
Meleagris_gallopavo 2872 19 205 258
Monodelphis_domestica 3049 142 76 87
Mus_musculus 3124 55 51 124
Neoceratodus_forsteri 2101 75 723 455
Notamacropus_eugenii 1169 29 514 1642
Oreochromis_niloticus 3275 20 25 34
Ornithorhynchus_anatinus 3075 36 141 102
Petromyzon_marinus 2275 59 193 827
Protopterus_annectens 2029 1130 105 90
Rana_temporaria 3088 74 76 116
Scyliorhinus_canicula 2977 102 106 169
Taeniopygia_guttata 3161 19 50 124
Takifugu_rubripes 3120 77 73 84
Xenopus_tropicalis 3231 34 30 59

Alignments

full

Location of alignment files:

results/alignments/full

Used aligner(s) and settings:
1. clustalo
Parsimony informative sites cutoff: 50

Number of alignments for clustalo: 16
Number of alignments for mafft: 16
Number of alignments for muscle: 16

Overview of individual full alignments:
clustalo
mafft
muscle
length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed
193525at7742_aligned.fas 652 25 179 617 35 659 25 180 625 34 690 25 178 655 35
359032at7742_aligned.fas 347 25 104 325 22 347 25 105 325 22 347 25 105 325 22
406935at7742_aligned.fas 292 25 75 276 16 299 25 80 283 16 305 25 81 289 16
97645at7742_aligned.fas 1237 24 290 1162 75 1320 24 287 1243 77 1399 24 291 1320 79
332227at7742_aligned.fas 554 23 169 508 46 552 23 168 506 46 565 23 166 519 46
361842at7742_aligned.fas 352 25 74 334 18 365 25 75 345 20 364 25 79 344 20
409625at7742_aligned.fas 244 25 69 234 10 245 25 67 233 12 246 25 67 234 12
33940at7742_aligned.fas 1351 25 102 1085 266 1394 25 111 1123 271 1397 25 103 1127 270
378120at7742_aligned.fas 266 25 116 216 50 277 25 118 227 50 291 25 105 241 50
409719at7742_aligned.fas 410 25 72 388 22 358 25 72 336 22 416 25 72 394 22
342641at7742_aligned.fas 364 25 127 324 40 368 25 130 327 41 374 25 128 333 41
403632at7742_aligned.fas 423 25 34 412 11 431 25 44 420 11 441 25 41 430 11
413149at7742_aligned.fas 232 25 75 226 6 253 25 85 247 6 236 25 78 230 6
353318at7742_aligned.fas 382 25 86 369 13 390 25 88 377 13 397 25 90 384 13
404316at7742_aligned.fas 262 25 66 221 41 255 25 66 214 41 271 25 65 230 41
42971at7742_aligned.fas 1327 23 448 1037 290 1351 23 462 1060 291 1372 23 464 1082 290

trimmed

Location of trimmed alignment files:

results/alignments/trimmed

Parsimony informative sites cutoff: 50


Number of trimmed alignments for clustalo-aliscore: 16
Number of trimmed alignments for clustalo-trimal: 16
Number of trimmed alignments for mafft-aliscore: 16
Number of trimmed alignments for mafft-trimal: 16
Number of trimmed alignments for muscle-aliscore: 16
Number of trimmed alignments for muscle-trimal: 16

Overview of individual trimmed alignments:
clustalo
clustalo
mafft
mafft
muscle
muscle
aliscore
trimal
aliscore
trimal
aliscore
trimal
alignment length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed
193525at7742_aligned_trimmed.fas 437 25 174 393 44 454 25 179 419 35 458 25 178 414 44 469 25 180 435 34 462 25 173 418 44 469 25 178 434 35
332227at7742_aligned_trimmed.fas 292 23 144 227 65 298 23 169 252 46 293 23 143 228 65 299 23 168 253 46 292 23 143 227 65 296 23 166 250 46
33940at7742_aligned_trimmed.fas 1113 25 101 800 313 1018 25 102 752 266 1129 25 110 808 321 1022 25 111 751 271 1107 25 102 788 319 1016 25 103 746 270
342641at7742_aligned_trimmed.fas 274 25 118 232 42 259 25 127 219 40 288 25 127 246 42 264 25 130 223 41 291 25 121 249 42 265 25 128 224 41
353318at7742_aligned_trimmed.fas 208 25 87 195 13 214 25 86 201 13 205 25 89 192 13 232 25 88 219 13 206 25 91 193 13 250 25 90 237 13
359032at7742_aligned_trimmed.fas 165 25 103 141 24 254 25 104 232 22 165 25 103 141 24 170 25 105 148 22 164 25 102 140 24 191 25 105 169 22
361842at7742_aligned_trimmed.fas 233 25 75 212 21 219 25 74 201 18 239 25 76 215 24 219 25 75 199 20 235 25 77 211 24 218 25 79 198 20
378120at7742_aligned_trimmed.fas 253 25 115 192 61 253 25 116 203 50 261 25 117 200 61 253 25 118 203 50 257 25 104 196 61 252 25 105 202 50
403632at7742_aligned_trimmed.fas 177 25 32 162 15 166 25 34 155 11 190 25 41 175 15 171 25 44 160 11 189 25 41 174 15 171 25 41 160 11
404316at7742_aligned_trimmed.fas 209 25 67 163 46 217 25 66 176 41 208 25 67 162 46 220 25 66 179 41 205 25 66 159 46 217 25 65 176 41
406935at7742_aligned_trimmed.fas 139 25 75 119 20 204 25 75 188 16 146 25 80 124 22 207 25 80 191 16 147 25 81 125 22 206 25 81 190 16
409625at7742_aligned_trimmed.fas 132 25 69 120 12 137 25 69 127 10 146 25 67 132 14 134 25 67 122 12 138 25 67 124 14 133 25 67 121 12
409719at7742_aligned_trimmed.fas 130 25 72 107 23 227 25 72 205 22 134 25 72 111 23 151 25 72 129 22 130 25 72 107 23 229 25 72 207 22
413149at7742_aligned_trimmed.fas 102 25 66 93 9 124 25 75 118 6 112 25 73 103 9 125 25 85 119 6 105 25 67 96 9 127 25 78 121 6
42971at7742_aligned_trimmed.fas 929 23 410 619 310 1016 23 448 726 290 940 23 413 629 311 998 23 462 707 291 940 23 429 630 310 1026 23 464 736 290
97645at7742_aligned_trimmed.fas 797 24 284 704 93 747 24 290 672 75 817 24 279 720 97 737 24 287 660 77 829 24 280 731 98 740 24 291 661 79

filtered

Location of filtered alignment files:

results/alignments/filtered

Parsimony informative sites cutoff: 50


Number of filtered alignments for clustalo-aliscore: 15
Number of filtered alignments for clustalo-trimal: 15
Number of filtered alignments for mafft-aliscore: 15
Number of filtered alignments for mafft-trimal: 15
Number of filtered alignments for muscle-aliscore: 15
Number of filtered alignments for muscle-trimal: 15

Overview of individual filtered alignments:
clustalo
clustalo
mafft
mafft
muscle
muscle
aliscore
trimal
aliscore
trimal
aliscore
trimal
alignment length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed length nseqs nparsimony nvariable nfixed
193525at7742_aligned_trimmed.fas 437 25 174 393 44 454 25 179 419 35 458 25 178 414 44 469 25 180 435 34 462 25 173 418 44 469 25 178 434 35
332227at7742_aligned_trimmed.fas 292 23 144 227 65 298 23 169 252 46 293 23 143 228 65 299 23 168 253 46 292 23 143 227 65 296 23 166 250 46
33940at7742_aligned_trimmed.fas 1113 25 101 800 313 1018 25 102 752 266 1129 25 110 808 321 1022 25 111 751 271 1107 25 102 788 319 1016 25 103 746 270
342641at7742_aligned_trimmed.fas 274 25 118 232 42 259 25 127 219 40 288 25 127 246 42 264 25 130 223 41 291 25 121 249 42 265 25 128 224 41
353318at7742_aligned_trimmed.fas 208 25 87 195 13 214 25 86 201 13 205 25 89 192 13 232 25 88 219 13 206 25 91 193 13 250 25 90 237 13
359032at7742_aligned_trimmed.fas 165 25 103 141 24 254 25 104 232 22 165 25 103 141 24 170 25 105 148 22 164 25 102 140 24 191 25 105 169 22
361842at7742_aligned_trimmed.fas 233 25 75 212 21 219 25 74 201 18 239 25 76 215 24 219 25 75 199 20 235 25 77 211 24 218 25 79 198 20
378120at7742_aligned_trimmed.fas 253 25 115 192 61 253 25 116 203 50 261 25 117 200 61 253 25 118 203 50 257 25 104 196 61 252 25 105 202 50
404316at7742_aligned_trimmed.fas 209 25 67 163 46 217 25 66 176 41 208 25 67 162 46 220 25 66 179 41 205 25 66 159 46 217 25 65 176 41
406935at7742_aligned_trimmed.fas 139 25 75 119 20 204 25 75 188 16 146 25 80 124 22 207 25 80 191 16 147 25 81 125 22 206 25 81 190 16
409625at7742_aligned_trimmed.fas 132 25 69 120 12 137 25 69 127 10 146 25 67 132 14 134 25 67 122 12 138 25 67 124 14 133 25 67 121 12
409719at7742_aligned_trimmed.fas 130 25 72 107 23 227 25 72 205 22 134 25 72 111 23 151 25 72 129 22 130 25 72 107 23 229 25 72 207 22
413149at7742_aligned_trimmed.fas 102 25 66 93 9 124 25 75 118 6 112 25 73 103 9 125 25 85 119 6 105 25 67 96 9 127 25 78 121 6
42971at7742_aligned_trimmed.fas 929 23 410 619 310 1016 23 448 726 290 940 23 413 629 311 998 23 462 707 291 940 23 429 630 310 1026 23 464 736 290
97645at7742_aligned_trimmed.fas 797 24 284 704 93 747 24 290 672 75 817 24 279 720 97 737 24 287 660 77 829 24 280 731 98 740 24 291 661 79

Modeltesting

Location of modeltesting files:

results/modeltest
Overview of individual modeltest results:
alignment clustalo-aliscore clustalo-trimal mafft-aliscore mafft-trimal muscle-aliscore muscle-trimal
193525at7742 JTT+G4 JTT+G4 JTT+G4 JTT+G4 JTT+G4 JTT+G4
332227at7742 JTT+G4 JTT+G4 JTT+G4 JTT+G4 JTT+G4 JTT+G4
33940at7742 VT+R2 VT+R2 JTT+R2 JTT+R2 JTT+R2 JTT+R2
342641at7742 LG+I+G4 LG+I+G4 LG+I+G4 LG+I+G4 LG+I+G4 LG+I+G4
353318at7742 JTT+G4 JTT+G4 JTT+G4 JTT+G4 JTT+G4 JTT+G4
359032at7742 LG+G4 JTT+I+G4 LG+G4 JTT+G4 LG+G4 JTT+G4
361842at7742 LG+G4 JTTDCMut+G4 LG+G4 JTTDCMut+G4 JTTDCMut+G4 JTTDCMut+G4
378120at7742 LG+G4 JTTDCMut+F+R3 LG+G4 JTTDCMut+F+R3 LG+G4 LG+G4
404316at7742 JTT+R2 JTT+R3 JTT+R2 JTT+R3 JTT+R2 JTT+R3
406935at7742 LG+G4 VT+G4 LG+G4 LG+G4 LG+G4 VT+G4
409625at7742 JTT+I+G4 JTT+I+G4 JTT+I+G4 JTT+I+G4 JTT+I+G4 JTT+I+G4
409719at7742 LG+G4 JTT+I+G4 LG+G4 JTTDCMut+G4 LG+G4 JTT+I+G4
413149at7742 JTTDCMut+G4 JTTDCMut+G4 JTTDCMut+G4 JTTDCMut+G4 JTTDCMut+G4 JTTDCMut+G4
42971at7742 JTT+I+G4 JTT+I+G4 JTT+I+G4 JTT+I+G4 JTT+I+G4 JTT+I+G4
97645at7742 JTT+R3 JTT+R3 JTT+R3 JTT+R3 JTT+R3 JTT+R3

Genetrees

Location of gene trees:

results/modeltest

Overview of mean bootstrap values per gene-tree:
Total number of gene trees for clustalo-aliscore: 15
Total number of gene trees for clustalo-trimal: 15
Total number of gene trees for mafft-aliscore: 15
Total number of gene trees for mafft-trimal: 15
Total number of gene trees for muscle-aliscore: 15
Total number of gene trees for muscle-trimal: 15
gene clustalo-aliscore clustalo-trimal mafft-aliscore mafft-trimal muscle-aliscore muscle-trimal
193525at7742 86 87 84 88 85 87
332227at7742 84 87 83 85 83 85
33940at7742 85 83 84 84 80 80
342641at7742 78 76 78 77 80 77
353318at7742 81 82 81 81 80 84
359032at7742 78 79 78 76 79 80
361842at7742 81 79 77 78 77 78
378120at7742 79 73 77 73 77 77
404316at7742 80 81 82 84 76 79
406935at7742 68 74 68 79 72 78
409625at7742 77 74 80 85 79 82
409719at7742 65 78 69 71 67 71
413149at7742 76 78 77 79 75 79
42971at7742 86 86 85 86 87 88
97645at7742 85 85 83 83 83 84

MLtree

Location of phylogenetic results:

results/phylogeny-*/

Overview of concatenated Maximum-likelihood phylogenies:
software aligner trimmer boostraps bootstrap-cutoff ngenes tree
iqtree clustalo aliscore 1000 0 15
iqtree clustalo aliscore 1000 50 15
iqtree clustalo aliscore 1000 60 15
iqtree clustalo aliscore 1000 70 13
iqtree clustalo aliscore 1000 80 8
iqtree clustalo trimal 1000 0 15
iqtree clustalo trimal 1000 50 15
iqtree clustalo trimal 1000 60 15
iqtree clustalo trimal 1000 70 15
iqtree clustalo trimal 1000 80 7
iqtree mafft aliscore 1000 0 15
iqtree mafft aliscore 1000 50 15
iqtree mafft aliscore 1000 60 15
iqtree mafft aliscore 1000 70 13
iqtree mafft aliscore 1000 80 8
iqtree mafft trimal 1000 0 15
iqtree mafft trimal 1000 50 15
iqtree mafft trimal 1000 60 15
iqtree mafft trimal 1000 70 15
iqtree mafft trimal 1000 80 8
iqtree muscle aliscore 1000 0 15
iqtree muscle aliscore 1000 50 15
iqtree muscle aliscore 1000 60 15
iqtree muscle aliscore 1000 70 14
iqtree muscle aliscore 1000 80 7
iqtree muscle trimal 1000 0 15
iqtree muscle trimal 1000 50 15
iqtree muscle trimal 1000 60 15
iqtree muscle trimal 1000 70 15
iqtree muscle trimal 1000 80 8
raxmlng clustalo aliscore 100 0 15
raxmlng clustalo aliscore 100 50 15
raxmlng clustalo aliscore 100 60 15
raxmlng clustalo aliscore 100 70 13
raxmlng clustalo aliscore 100 80 8
raxmlng clustalo trimal 100 0 15
raxmlng clustalo trimal 100 50 15
raxmlng clustalo trimal 100 60 15
raxmlng clustalo trimal 100 70 15
raxmlng clustalo trimal 100 80 7
raxmlng mafft aliscore 100 0 15
raxmlng mafft aliscore 100 50 15
raxmlng mafft aliscore 100 60 15
raxmlng mafft aliscore 100 70 13
raxmlng mafft aliscore 100 80 8
raxmlng mafft trimal 100 0 15
raxmlng mafft trimal 100 50 15
raxmlng mafft trimal 100 60 15
raxmlng mafft trimal 100 70 15
raxmlng mafft trimal 100 80 8
raxmlng muscle aliscore 100 0 15
raxmlng muscle aliscore 100 50 15
raxmlng muscle aliscore 100 60 15
raxmlng muscle aliscore 100 70 14
raxmlng muscle aliscore 100 80 7
raxmlng muscle trimal 100 0 15
raxmlng muscle trimal 100 50 15
raxmlng muscle trimal 100 60 15
raxmlng muscle trimal 100 70 15
raxmlng muscle trimal 100 80 8

Speciestree

Location of phylogenetic results:

results/phylogeny-*/

Overview of species-tree phylogenies:
software aligner trimmer bootstrap-cutoff ngenes tree
astral clustalo aliscore 0 15
astral clustalo aliscore 50 15
astral clustalo aliscore 60 15
astral clustalo aliscore 70 13
astral clustalo aliscore 80 8
astral clustalo trimal 0 15
astral clustalo trimal 50 15
astral clustalo trimal 60 15
astral clustalo trimal 70 15
astral clustalo trimal 80 7
astral mafft aliscore 0 15
astral mafft aliscore 50 15
astral mafft aliscore 60 15
astral mafft aliscore 70 13
astral mafft aliscore 80 8
astral mafft trimal 0 15
astral mafft trimal 50 15
astral mafft trimal 60 15
astral mafft trimal 70 15
astral mafft trimal 80 8
astral muscle aliscore 0 15
astral muscle aliscore 50 15
astral muscle aliscore 60 15
astral muscle aliscore 70 14
astral muscle aliscore 80 7
astral muscle trimal 0 15
astral muscle trimal 50 15
astral muscle trimal 60 15
astral muscle trimal 70 15
astral muscle trimal 80 8

Log

## Thu Jul  7 15:40:41 CEST 2022 - Pipeline part 1 (orthology) done.
## Thu Jul  7 15:41:32 CEST 2022 - BUSCO files will be filtered on a per-sample basis. This could lower the number of species in the final tree.
## Thu Jul  7 15:41:34 CEST 2022 - Number of BUSCO sequence files: 16
## Thu Jul  7 15:41:34 CEST 2022 - Number of deduplicated BUSCO sequence files: 16
## Thu Jul  7 15:41:34 CEST 2022 - Pipeline part filter-orthology done.
## Sat Jan 21 17:38:39 CET 2023 - Pipeline part 2 (align) done.
## Sat Jan 21 17:40:00 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 42971at7742
## Sat Jan 21 17:40:00 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 42971at7742
## Sat Jan 21 17:40:01 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 97645at7742
## Sat Jan 21 17:40:01 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 97645at7742
## Sat Jan 21 17:40:03 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 332227at7742
## Sat Jan 21 17:40:03 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 332227at7742
## Sat Jan 21 17:40:03 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 33940at7742
## Sat Jan 21 17:40:03 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 33940at7742
## Sat Jan 21 17:40:03 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 332227at7742
## Sat Jan 21 17:40:03 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 332227at7742
## Sat Jan 21 17:40:06 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 193525at7742
## Sat Jan 21 17:40:06 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 193525at7742
## Sat Jan 21 17:40:06 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 97645at7742
## Sat Jan 21 17:40:06 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 97645at7742
## Sat Jan 21 17:40:07 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 42971at7742
## Sat Jan 21 17:40:07 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 42971at7742
## Sat Jan 21 17:40:07 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 33940at7742
## Sat Jan 21 17:40:07 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 33940at7742
## Sat Jan 21 17:40:07 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 42971at7742
## Sat Jan 21 17:40:07 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 42971at7742
## Sat Jan 21 17:40:08 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 193525at7742
## Sat Jan 21 17:40:08 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 332227at7742
## Sat Jan 21 17:40:08 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 332227at7742
## Sat Jan 21 17:40:08 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 193525at7742
## Sat Jan 21 17:40:08 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 403632at7742
## Sat Jan 21 17:40:08 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 403632at7742
## Sat Jan 21 17:40:08 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 403632at7742
## Sat Jan 21 17:40:08 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 403632at7742
## Sat Jan 21 17:40:08 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 33940at7742
## Sat Jan 21 17:40:08 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409719at7742
## Sat Jan 21 17:40:09 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 33940at7742
## Sat Jan 21 17:40:09 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409719at7742
## Sat Jan 21 17:40:09 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 353318at7742
## Sat Jan 21 17:40:09 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 353318at7742
## Sat Jan 21 17:40:09 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 97645at7742
## Sat Jan 21 17:40:09 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 193525at7742
## Sat Jan 21 17:40:09 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 97645at7742
## Sat Jan 21 17:40:09 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 193525at7742
## Sat Jan 21 17:40:09 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 353318at7742
## Sat Jan 21 17:40:09 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 353318at7742
## Sat Jan 21 17:40:10 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 403632at7742
## Sat Jan 21 17:40:10 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 403632at7742
## Sat Jan 21 17:40:10 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409719at7742
## Sat Jan 21 17:40:10 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409719at7742
## Sat Jan 21 17:40:12 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 342641at7742
## Sat Jan 21 17:40:12 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 342641at7742
## Sat Jan 21 17:40:12 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 342641at7742
## Sat Jan 21 17:40:12 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 342641at7742
## Sat Jan 21 17:40:12 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 361842at7742
## Sat Jan 21 17:40:12 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 361842at7742
## Sat Jan 21 17:40:12 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 361842at7742
## Sat Jan 21 17:40:12 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 361842at7742
## Sat Jan 21 17:40:13 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 353318at7742
## Sat Jan 21 17:40:13 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 353318at7742
## Sat Jan 21 17:40:14 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 359032at7742
## Sat Jan 21 17:40:14 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 359032at7742
## Sat Jan 21 17:40:14 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 342641at7742
## Sat Jan 21 17:40:14 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 342641at7742
## Sat Jan 21 17:40:14 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409719at7742
## Sat Jan 21 17:40:14 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409719at7742
## Sat Jan 21 17:40:15 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 359032at7742
## Sat Jan 21 17:40:15 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 359032at7742
## Sat Jan 21 17:40:15 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 361842at7742
## Sat Jan 21 17:40:15 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 361842at7742
## Sat Jan 21 17:40:16 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 406935at7742
## Sat Jan 21 17:40:16 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 359032at7742
## Sat Jan 21 17:40:16 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 406935at7742
## Sat Jan 21 17:40:16 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 359032at7742
## Sat Jan 21 17:40:18 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 406935at7742
## Sat Jan 21 17:40:18 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 406935at7742
## Sat Jan 21 17:40:19 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 406935at7742
## Sat Jan 21 17:40:19 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 406935at7742
## Sat Jan 21 17:40:19 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 378120at7742
## Sat Jan 21 17:40:19 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 378120at7742
## Sat Jan 21 17:40:19 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 404316at7742
## Sat Jan 21 17:40:19 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 404316at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 404316at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 404316at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 404316at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 378120at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 404316at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 378120at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 413149at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 413149at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 378120at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 378120at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 413149at7742
## Sat Jan 21 17:40:20 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 413149at7742
## Sat Jan 21 17:40:21 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409625at7742
## Sat Jan 21 17:40:21 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409625at7742
## Sat Jan 21 17:40:21 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409625at7742
## Sat Jan 21 17:40:21 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409625at7742
## Sat Jan 21 17:40:21 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 413149at7742
## Sat Jan 21 17:40:21 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 413149at7742
## Sat Jan 21 17:40:22 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409625at7742
## Sat Jan 21 17:40:22 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409625at7742
## Sat Jan 21 17:40:23 CET 2023 - Number of alignments (mafft): 16
## Sat Jan 21 17:40:23 CET 2023 - Number of trimmed alignments (mafft - trimal): 16
## Sat Jan 21 17:40:23 CET 2023 - Number of alignments (mafft - trimal) after filtering: 15
## Sat Jan 21 17:40:30 CET 2023 - Number of alignments (clustalo): 16
## Sat Jan 21 17:40:30 CET 2023 - Number of trimmed alignments (clustalo - trimal): 16
## Sat Jan 21 17:40:30 CET 2023 - Number of alignments (clustalo - trimal) after filtering: 15
## Sat Jan 21 17:40:30 CET 2023 - Number of alignments (muscle): 16
## Sat Jan 21 17:40:30 CET 2023 - Number of trimmed alignments (muscle - trimal): 16
## Sat Jan 21 17:40:30 CET 2023 - Number of alignments (muscle - trimal) after filtering: 15
## Sat Jan 21 17:40:36 CET 2023 - Number of alignments (mafft): 16
## Sat Jan 21 17:40:36 CET 2023 - Number of trimmed alignments (mafft - aliscore): 16
## Sat Jan 21 17:40:36 CET 2023 - Number of alignments (muscle): 16
## Sat Jan 21 17:40:36 CET 2023 - Number of trimmed alignments (muscle - aliscore): 16
## Sat Jan 21 17:40:36 CET 2023 - Number of alignments (mafft - aliscore) after filtering: 15
## Sat Jan 21 17:40:36 CET 2023 - Number of alignments (muscle - aliscore) after filtering: 15
## Sat Jan 21 17:40:36 CET 2023 - Number of alignments (clustalo): 16
## Sat Jan 21 17:40:36 CET 2023 - Number of trimmed alignments (clustalo - aliscore): 16
## Sat Jan 21 17:40:36 CET 2023 - Number of alignments (clustalo - aliscore) after filtering: 15
## Sat Jan 21 17:40:43 CET 2023 - Pipeline part filter_align done.
## Sat Jan 21 17:50:17 CET 2023 - Pipeline part modeltest (model) done.
## Sat Jan 21 17:55:06 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Sat Jan 21 17:55:06 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Sat Jan 21 17:55:06 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Sat Jan 21 17:55:06 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Sat Jan 21 17:55:06 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Sat Jan 21 17:55:06 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Sat Jan 21 17:55:06 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Sat Jan 21 17:55:06 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Sat Jan 21 17:55:06 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Sat Jan 21 17:55:06 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Sat Jan 21 17:55:07 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Sat Jan 21 17:55:07 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Sat Jan 21 17:55:07 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Sat Jan 21 17:55:07 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Sat Jan 21 17:55:07 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Sat Jan 21 17:55:07 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Sat Jan 21 17:55:07 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Sat Jan 21 17:55:07 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Sat Jan 21 17:55:07 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Sat Jan 21 17:55:07 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Sat Jan 21 17:55:08 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Sat Jan 21 17:55:08 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Sat Jan 21 17:55:08 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Sat Jan 21 17:55:08 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Sat Jan 21 17:55:08 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Sat Jan 21 17:55:08 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Sat Jan 21 17:55:08 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Sat Jan 21 17:55:08 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Sat Jan 21 17:55:08 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Sat Jan 21 17:55:08 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Sat Jan 21 17:55:22 CET 2023 - Speciestree reconstruction done.
## Sat Jan 21 17:56:04 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (60) before creating concatenated alignment
## Sat Jan 21 17:56:04 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (60) before creating concatenated alignment
## Sat Jan 21 17:56:04 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (80) before creating concatenated alignment
## Sat Jan 21 17:56:04 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (60) before creating concatenated alignment
## Sat Jan 21 17:56:04 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (0) before creating concatenated alignment
## Sat Jan 21 17:56:04 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (0) before creating concatenated alignment
## Sat Jan 21 17:56:04 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (80) before creating concatenated alignment
## Sat Jan 21 17:56:04 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (80) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:04 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (0) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:04 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (70) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:11 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:11 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:11 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:11 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:11 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:11 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:11 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:11 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:12 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:12 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:12 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (70) before creating concatenated alignment
## Sat Jan 21 17:56:12 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (50) before creating concatenated alignment
## Sat Jan 21 17:56:12 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (50) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:12 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (50) before creating concatenated alignment
## Sat Jan 21 17:56:12 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (70) before creating concatenated alignment
## Sat Jan 21 17:56:12 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (60) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:14 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:14 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:14 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:15 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:15 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:15 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (60) before creating concatenated alignment
## Sat Jan 21 17:56:16 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (80) before creating concatenated alignment
## Sat Jan 21 17:56:16 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:16 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (60) before creating concatenated alignment
## Sat Jan 21 17:56:16 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (80) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:16 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (0) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:16 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:16 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:16 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:16 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:17 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:17 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (80) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:18 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:18 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (70) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:18 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (0) before creating concatenated alignment
## Sat Jan 21 17:56:18 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (0) before creating concatenated alignment
## Sat Jan 21 17:56:18 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (50) before creating concatenated alignment
## Sat Jan 21 17:56:18 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (50) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:19 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:19 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (50) before creating concatenated alignment
## Sat Jan 21 17:56:19 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (70) before creating concatenated alignment
## Sat Jan 21 17:56:19 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (70) before creating concatenated alignment
## Sat Jan 21 17:56:19 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:19 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:19 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:19 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Sat Jan 21 17:56:19 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:19 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 17:56:19 CET 2023 - nexus file for iqtree written.
## Sat Jan 21 18:08:20 CET 2023 - Pipeline part 3 (tree) done.
## Sat Jan 21 18:15:45 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 80 before creating concatenated alignment
## Sat Jan 21 18:15:45 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 60 before creating concatenated alignment
## Sat Jan 21 18:15:45 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 80 before creating concatenated alignment
## Sat Jan 21 18:15:45 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 50 before creating concatenated alignment
## Sat Jan 21 18:15:45 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 70 before creating concatenated alignment
## Sat Jan 21 18:15:45 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 70 before creating concatenated alignment
## Sat Jan 21 18:15:45 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 60 before creating concatenated alignment
## Sat Jan 21 18:15:45 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 60 before creating concatenated alignment
## Sat Jan 21 18:15:45 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 60 before creating concatenated alignment
## Sat Jan 21 18:15:45 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 50 before creating concatenated alignment
## Sat Jan 21 18:15:55 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 80 before creating concatenated alignment
## Sat Jan 21 18:15:56 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 0 before creating concatenated alignment
## Sat Jan 21 18:15:56 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 0 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 0 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 80 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 0 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 70 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 70 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 50 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 50 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 0 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 80 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 70 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 50 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:57 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 80 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 60 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 60 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 70 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 0 before creating concatenated alignment
## Sat Jan 21 18:15:57 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 50 before creating concatenated alignment
## Sat Jan 21 18:15:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:59 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:59 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:59 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:59 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:15:59 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:16:00 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:16:00 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:16:00 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:16:00 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:16:00 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:16:00 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:16:01 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:16:01 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sat Jan 21 18:16:01 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sun Jan 22 14:17:01 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sun Jan 22 14:17:01 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sun Jan 22 14:17:01 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sun Jan 22 14:17:01 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sun Jan 22 14:17:01 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sun Jan 22 14:17:01 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sun Jan 22 14:17:01 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sun Jan 22 14:17:01 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Sun Jan 22 19:46:44 CET 2023 - Pipeline part 3 (tree) done.